San Diego  Federal prosecutors now say the former head of the labor union for U.S. Border Patrol agents was defrauding the union with bogus wage and travel claims for close to two decades.

The allegation is the latest in the case against T.J. Bonner, who led the National Border Patrol Council from 1993 until he retired in 2010.

Bonner, a longtime Campo resident, was indicted last year in San Diego federal court on conspiracy and wire fraud charges. Prosecutors said that he billed personal expenses for wages, travel, meals, tickets to sporting events and other items to the union.

His reimbursement claims would say he had incurred the expenses while working on union business. The government said he was not working for the union, and in many instances was actually visiting a mistress outside of Chicago.

Prosecutors filed their response this month to legal motions filed by Bonner’s lawyer to dismiss the case. While the indictment covers from 2004 to 2010 only, in the new filing prosecutors said Bonner’s fraud began more than a decade before that.

The union policies related to being paid for “lost wages” were put in place in 1993, just after Bonner took over as union president, the filing says. The time frame for the investigation was expanded following a search in March 2012 of Bonner’s home, which yielded a huge amount of data stored in files, computers, and hard drives.

The original search warrant covered from 2004 onward, but in December prosecutors got a second search warrant that expanded the search.

“We believe he was engaging in this type of conduct back to 1993,” said Assistant U.S. Attorney Mark Conover.

Bonner has pleaded not guilty. He has said his blunt-spoken leadership on behalf of the union over the years earned him enemies, and the probe is retaliation for that. His lawyer, Eugene Iredale, said in January that the investigation was “completely unjustified” and did not even comply with Department of Homeland Security rules governing how invesitgations are conducted.

The document filed by prosecutors also provided more details about the wage fraud allegations. Conover and Assistant U.S. Attorney Robert Huie wrote that each year from 2004 to 2010 Bonner put in lost wage compensation claims for every Sunday, every federal holiday, most nights, 14.5 hours of overtime for each pay period and payment for annual leave.

In 2008, he put in a voucher in March for all of the lost wages pay for the entire year, prosecutors said, attaching a spread sheet claiming holiday and night pay months in advance.

The secretary-treasurer of the union, who is identified as a co-conspirator but has not been indicted, approved the vouchers. He is identified as Jospeh Bradley, who served in the union post for 32 years, in an affidavit for a search warrant of Bonner’s home.

Bradley told investigators with the internal affairs unit for U.S. Customs and Border Protection that he never questioned Bonner’s payment requests and that “he just trusted Bonner to be honest,” the affidavit said.

The court records outline a portrait of Bonner at odds with the crisp, hard-charging, high-profile personality he projected as the combative head of the union.

Bonner worked mostly from his home in Campo, which was searched as part of the investigation in 2012. “He was accountable to no one — not a fellow Union officer not a Border Patrol supervisor, and not even an assistant — on a daily basis for his whereabouts and activities,” wrote prosecutors Mark Conover and Robert Huie.

When agents searched Bonner’s home, they were confronted with an extraordinary scene. The home was “in a state of extreme disarray,” according to court records. Rooms in the home were jammed with boxes, magazine, bedding, papers — stacked ceiling-high in some rooms.

There were open trash cans, and some surfaces were covered with thick layers of dust and what appeared to be animal hair.

“Within minutes, officers were coughing and talking turns going outside for fresh air,” the prosecutors wrote. Photographs attached to the motion show rooms jammed with boxes and piles of clothing and other items.

Iredale, Bonner’s lawyer, has challenged how the search was conducted. He said any materials that come before 2004 that were seized should be thrown out because they went beyond the scope of the search warrant.

The government argued that the evidence was intermingled in the chaos of Bonner’s home. Boxes labeled after 2004 contained information from before then, and it was impossible to sort it out on the spot. They also said it was inevitable that the pre-2004 evidence would be found, and that in any event the government got a new search warrant expanding the scope of the probe before any of the pre-2004 evidence was analyzed.

The investigation into Bonner began after he submitted 52 vouchers to the government for payment of his travel expenses on union-related business between 2004 and 2009, according to the search warrant affidavit. Customs and Border Protection denied the claims because they didn’t conform to agency policy. But the claims also raised suspicion, and that launched the probe that eventually led to the indictment.